My Introduction

Course notes from the Data Vizualization with ggplot2 (Part 1) course on DataCamp

Whats Covered

Introduction
Data
Aesthetics
Geometries
qplot and wrap-up

Aditional Resources

Introduction

Data visualization is statistics and graphical designed combined
- The function is to accurately represent the data
- The form is important to communicate the point well
Choose your audience first
- Exploratory plots are for yourself and maye colleagues and meant to confirm and analyze
- Explanatory plots are for a reader and are meant to inform and persuade

– Explore and Explain

Exploratory plots are
- meant for a specialist audience
- usaually data-heavy
- rough first drafts with less attention to making it pretty

– Exploring ggplot2, part 1

# Load the ggplot2 package
library(ggplot2)

# Explore the mtcars data frame with str()
str(mtcars)

## 'data.frame':    32 obs. of  11 variables:
##  $ mpg : num  21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 ...
##  $ cyl : num  6 6 4 6 8 6 8 4 4 6 ...
##  $ disp: num  160 160 108 258 360 ...
##  $ hp  : num  110 110 93 110 175 105 245 62 95 123 ...
##  $ drat: num  3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 ...
##  $ wt  : num  2.62 2.88 2.32 3.21 3.44 ...
##  $ qsec: num  16.5 17 18.6 19.4 17 ...
##  $ vs  : num  0 0 1 1 0 1 0 1 1 1 ...
##  $ am  : num  1 1 1 0 0 0 0 0 0 0 ...
##  $ gear: num  4 4 4 3 3 3 3 4 4 4 ...
##  $ carb: num  4 4 1 1 2 1 4 2 2 4 ...

# Execute the following command
ggplot(mtcars, aes(x = cyl, y = mpg)) +
  geom_point()

– Exploring ggplot2, part 2

We need to tell ggplot2 that cyl is a categorical variable by wrapping it in factor()

# Load the ggplot2 package
library(ggplot2)

# Change the command below so that cyl is treated as factor
ggplot(mtcars, aes(x = factor(cyl), y = mpg)) +
  geom_point()

Grammar of Graphics

Leland Wilkinson, Grammar of Graphics, 1999
2 principles
- graphics are made up of distinct layers of the grammatical elements
- meanigful plots are build around appropriate asthetical mappings
Layers
- The first 3 layers are essential for a plot.
- The last 4 are optional
- This course focuses on the first 3 layers
Each of these layers has specific elements that can be added or manipulated to create a plot
- this is just a sample of some of the elements in each layer to get the jist

– Exporing ggplot2, part 3

# A scatter plot has been made for you
ggplot(mtcars, aes(x = wt, y = mpg)) +
  geom_point()

# Replace ___ with the correct column
ggplot(mtcars, aes(x = wt, y = mpg, color = disp)) +
  geom_point()

# Replace ___ with the correct column
ggplot(mtcars, aes(x = wt, y = mpg, size = disp)) +
  geom_point()

– Understanding variables

some aestethics, like color can be mapped to either a discreate or continuous variable
- for example you can use a qualitative color scale for discrete data or a sequential color scale for continuous data
but other aesthetics, like shape, only make sense on a discreate variable
- i.e. there is no continuous variation between shapes.

ggplot(mtcars, aes(x = wt, y = mpg, shape = disp)) +
  geom_point()

## Error: A continuous variable can not be mapped to shape

ggplot2

Lets take a look at an example plot that uses all the layers
- I have noted each layer with comments
- Only the first 3 layers (data, aesthetics, geometry) are required to get a plot
This is a nice example of the big picture
We will go into a lot more detail on the first 3 layers in the rest of this class

str(iris)

## 'data.frame':    150 obs. of  5 variables:
##  $ Sepal.Length: num  5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...
##  $ Sepal.Width : num  3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ...
##  $ Petal.Length: num  1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...
##  $ Petal.Width : num  0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...
##  $ Species     : Factor w/ 3 levels "setosa","versicolor",..: 1 1 1 1 1 1 1 1 1 1 ...

levels(iris$Species) <- c("Setosa", "Versicolor", "Virginica")

## Data and Aesthetics Layer (essential)
p <- ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width)) + 
  
  ## Geometries Layer (essential)
  geom_jitter(alpha = 0.6)
p

p <- p +  
  ## Facets (optional)
  facet_grid(. ~ Species) +

  ## Statistics (optional)
  stat_smooth(method = "lm", se = F, col = "red") + 
  
  ## Coordinates Layer (optional)
  scale_y_continuous("Sepal Width (cm)", limits = c(2,5), expand = c(0,0)) + 
  scale_x_continuous("Sepal Length (cm)", limits = c(4,8), expand = c(0,0)) + 
  coord_equal()
p

p <- p + 
  ## Theme Layer (optional)
  theme(panel.background = element_blank(),
        plot.background = element_blank(),
        legend.background = element_blank(), 
        legend.key = element_blank(), 
        strip.background = element_blank(), 
        axis.text = element_text(colour = "black"), 
        axis.ticks = element_line(colour = "black"), 
        panel.grid.major = element_blank(), 
        panel.grid.minor = element_blank(), 
        axis.line = element_line(colour = "black"), 
        strip.text = element_blank(), 
        panel.margin = unit(1, "lines")
        )
p

– Exploring ggplot2, part 4

# Explore the diamonds data frame with str()
str(diamonds)

## Classes 'tbl_df', 'tbl' and 'data.frame':    53940 obs. of  10 variables:
##  $ carat  : num  0.23 0.21 0.23 0.29 0.31 0.24 0.24 0.26 0.22 0.23 ...
##  $ cut    : Ord.factor w/ 5 levels "Fair"<"Good"<..: 5 4 2 4 2 3 3 3 1 3 ...
##  $ color  : Ord.factor w/ 7 levels "D"<"E"<"F"<"G"<..: 2 2 2 6 7 7 6 5 2 5 ...
##  $ clarity: Ord.factor w/ 8 levels "I1"<"SI2"<"SI1"<..: 2 3 5 4 2 6 7 3 4 5 ...
##  $ depth  : num  61.5 59.8 56.9 62.4 63.3 62.8 62.3 61.9 65.1 59.4 ...
##  $ table  : num  55 61 65 58 58 57 57 55 61 61 ...
##  $ price  : int  326 326 327 334 335 336 336 337 337 338 ...
##  $ x      : num  3.95 3.89 4.05 4.2 4.34 3.94 3.95 4.07 3.87 4 ...
##  $ y      : num  3.98 3.84 4.07 4.23 4.35 3.96 3.98 4.11 3.78 4.05 ...
##  $ z      : num  2.43 2.31 2.31 2.63 2.75 2.48 2.47 2.53 2.49 2.39 ...

# Add geom_point() with +
ggplot(diamonds, aes(x = carat, y = price)) +
  geom_point()

# Add geom_point() and geom_smooth() with +
ggplot(diamonds, aes(x = carat, y = price)) +
  geom_point() + 
  geom_smooth()

– Exploring ggplot2, part 5

# 1 - The plot you created in the previous exercise
# ggplot(diamonds, aes(x = carat, y = price)) +
#   geom_point() +
#   geom_smooth()

# 2 - Copy the above command but show only the smooth line
ggplot(diamonds, aes(x = carat, y = price)) +
  geom_smooth()

# 3 - Copy the above command and assign the correct value to col in aes()
ggplot(diamonds, aes(x = carat, y = price, color = clarity)) +
  geom_smooth()

# 4 - Keep the color settings from previous command. Plot only the points with argument alpha.
ggplot(diamonds, aes(x = carat, y = price, color = clarity)) +
  geom_point(alpha = .4)

– Understanding the grammar, part 1

# Create the object containing the data and aes layers: dia_plot
dia_plot <- ggplot(diamonds, aes(x = carat, y = price))

# Add a geom layer with + and geom_point()
dia_plot + geom_point()

# Add the same geom layer, but with aes() inside
dia_plot + geom_point(aes(color = clarity))

– Understanding the grammar, part 2

# 1 - The dia_plot object has been created for you
dia_plot <- ggplot(diamonds, aes(x = carat, y = price))

# 2 - Expand dia_plot by adding geom_point() with alpha set to 0.2
dia_plot <- dia_plot + geom_point(alpha = 0.2)

# 3 - Plot dia_plot with additional geom_smooth() with se set to FALSE
dia_plot + geom_smooth(se = F)

# 4 - Copy the command from above and add aes() with the correct mapping to geom_smooth()
dia_plot + geom_smooth(aes(col = clarity), se = F)

Data

Objects and Layers

The structure of our data will influence how we plot it
- In general we should start with tidy data and then spread a variable if needed for a specific plot
The base plotting system has many limitations including
- Plot does not get redrawn when adding more data. points will not bee seen if outside the original scale
- plotisdearn as an image and not returned as an object that we can add to
- Need to manually add legend
- No unified framework for ploting. Its just a bunch of different chart commands

– base package and ggplot2, part 1 - plot

You can set the color based on a factor variable
- This is kind of a trick because the factors are integers 1 and 2 underneath. Thats the only reason it works.

# Plot the correct variables of mtcars
plot(mtcars$wt, mtcars$mpg, col = mtcars$cyl)

# Change cyl inside mtcars to a factor
mtcars$fcyl <- as.factor(mtcars$cyl)

# Make the same plot as in the first instruction
plot(mtcars$wt, mtcars$mpg, col = mtcars$fcyl)

– base package and ggplot2, part 2 - lm

Its a bit cumbersome to get multiple linear models onto the chart
- the lms need to be calculated separately and wrapped into the abline function with lapply. wah
- Also the legend is totally manual. boo

# Use lm() to calculate a linear model and save it as carModel
carModel <- lm(mpg ~ wt, data = mtcars)

# Basic plot
mtcars$cyl <- as.factor(mtcars$cyl)
plot(mtcars$wt, mtcars$mpg, col = mtcars$cyl)

# Call abline() with carModel as first argument and set lty to 2
abline(carModel, lty = 2)

# Plot each subset efficiently with lapply
# You don't have to edit this code
plot(mtcars$wt, mtcars$mpg, col = mtcars$cyl)

## this prints out a bunch of null values in list because nothing is returned from the abline function
## I have added results='hide' to prevent all that printing in the notebook
lapply(mtcars$cyl, function(x) {
  abline(lm(mpg ~ wt, mtcars, subset = (cyl == x)), col = x)
  })

# This code will draw the legend of the plot
# You don't have to edit this code
legend(x = 5, y = 33, legend = levels(mtcars$cyl),
       col = 1:3, pch = 1, bty = "n")

– base package and ggplot2, part 3

# Plot 1: add geom_point() to this command to create a scatter plot
ggplot(mtcars, aes(x = wt, y = mpg, col = cyl)) +
  geom_point()  # Fill in using instructions Plot 1

# Plot 2: include the lines of the linear models, per cyl
ggplot(mtcars, aes(x = wt, y = mpg, col = cyl)) +
  geom_point() + # Copy from Plot 1
  geom_smooth(method = 'lm', se = F)   # Fill in using instructions Plot 2

# Plot 3: include a lm for the entire dataset in its whole
ggplot(mtcars, aes(x = wt, y = mpg, col = cyl)) + 
  geom_point() + # Copy from Plot 2
  geom_smooth(method = 'lm', se = F) + # Copy from Plot 2
  geom_smooth(aes(group = 1), method = 'lm', se = F, linetype = 2)   # Fill in using instructions Plot 3

– ggplot2 compared to base package

ggplot2 has many advantages over the base R graphics system. Some things include:
- it creates plotting objects, which can be manipulated
- it takes care of a lot of the leg work for you, such as choosing nice color pallettes and making legends
- it is built upon the grammar of graphics plotting philosophy, making it more flexible and intuitive for understanding the relationship between your visuals and your data

Tidy Data

In general we should start with tidy data and then spread a variable if needed for a specific plot
The exercises here are backwards. they have you plot first, then create the dataset needed in the next exercise.
- I will flip them so it works

– Variables to visuals, tidy dataset

# Load the tidyr package
library(tidyr)

str(iris)

## 'data.frame':    150 obs. of  5 variables:
##  $ Sepal.Length: num  5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...
##  $ Sepal.Width : num  3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ...
##  $ Petal.Length: num  1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...
##  $ Petal.Width : num  0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...
##  $ Species     : Factor w/ 3 levels "Setosa","Versicolor",..: 1 1 1 1 1 1 1 1 1 1 ...

# Fill in the ___ to produce to the correct iris.tidy dataset
iris.tidy <- iris %>%
  gather(key, Value, -Species) %>%
  separate(key, c("Part", "Measure"), "\\.")
  
str(iris.tidy)

## 'data.frame':    600 obs. of  4 variables:
##  $ Species: Factor w/ 3 levels "Setosa","Versicolor",..: 1 1 1 1 1 1 1 1 1 1 ...
##  $ Part   : chr  "Sepal" "Sepal" "Sepal" "Sepal" ...
##  $ Measure: chr  "Length" "Length" "Length" "Length" ...
##  $ Value  : num  5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...

– Variables to visuals, tidy chart

Because length and width are in a column, we can easily split on this variable in the facet_grid

# Think about which dataset you would use to get the plot shown right
# Fill in the ___ to produce the plot given to the right
ggplot(iris.tidy, aes(x = Species, y = Value, col = Part)) +
  geom_jitter() +
  facet_grid(. ~ Measure)

– Variables to visuals, wide dataset

# Add column with unique ids (don't need to change)
iris$Flower <- 1:nrow(iris)

# Fill in the ___ to produce to the correct iris.wide dataset
iris.wide <- iris %>%
  gather(key, value, -Flower, -Species) %>%
  separate(key, c("Part", "Measure"), "\\.") %>%
  spread(Measure, value)

– Variables to visuals, wide chart

Now, if we want to compare length vs width on the x and y axis we need to have them in sepeate columns so we can assign one variable to each aesthetic x and y

# The 3 data frames (iris, iris.wide and iris.tidy) are available in your environment
# Execute head() on iris, iris.wide and iris.tidy (in that order)
head(iris)

##   Sepal.Length Sepal.Width Petal.Length Petal.Width Species Flower
## 1          5.1         3.5          1.4         0.2  Setosa      1
## 2          4.9         3.0          1.4         0.2  Setosa      2
## 3          4.7         3.2          1.3         0.2  Setosa      3
## 4          4.6         3.1          1.5         0.2  Setosa      4
## 5          5.0         3.6          1.4         0.2  Setosa      5
## 6          5.4         3.9          1.7         0.4  Setosa      6

head(iris.tidy)

##   Species  Part Measure Value
## 1  Setosa Sepal  Length   5.1
## 2  Setosa Sepal  Length   4.9
## 3  Setosa Sepal  Length   4.7
## 4  Setosa Sepal  Length   4.6
## 5  Setosa Sepal  Length   5.0
## 6  Setosa Sepal  Length   5.4

head(iris.wide)

##   Species Flower  Part Length Width
## 1  Setosa      1 Petal    1.4   0.2
## 2  Setosa      1 Sepal    5.1   3.5
## 3  Setosa      2 Petal    1.4   0.2
## 4  Setosa      2 Sepal    4.9   3.0
## 5  Setosa      3 Petal    1.3   0.2
## 6  Setosa      3 Sepal    4.7   3.2

# Think about which dataset you would use to get the plot shown right
# Fill in the ___ to produce the plot given to the right
ggplot(iris.wide, aes(x = Length, y = Width, color = Part)) +
  geom_jitter() +
  facet_grid(. ~ Species)

Aesthetics

Visible Aesthetics

Aestetics are mappings of a variable onto an axis, shape, color, size, etc
- They are called in the aes() function
Attributes are set on all elements of a variable, regardless of its individual values
- Setting all the points to be a shape of square and color red is an example of this
- These are set in the geom layer
Here are some of the most common aesthetics

– All about aesthetics, part 1

str(mtcars)

## 'data.frame':    32 obs. of  12 variables:
##  $ mpg : num  21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 ...
##  $ cyl : Factor w/ 3 levels "4","6","8": 2 2 1 2 3 2 3 1 1 2 ...
##  $ disp: num  160 160 108 258 360 ...
##  $ hp  : num  110 110 93 110 175 105 245 62 95 123 ...
##  $ drat: num  3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 ...
##  $ wt  : num  2.62 2.88 2.32 3.21 3.44 ...
##  $ qsec: num  16.5 17 18.6 19.4 17 ...
##  $ vs  : num  0 0 1 1 0 1 0 1 1 1 ...
##  $ am  : num  1 1 1 0 0 0 0 0 0 0 ...
##  $ gear: num  4 4 4 3 3 3 3 4 4 4 ...
##  $ carb: num  4 4 1 1 2 1 4 2 2 4 ...
##  $ fcyl: Factor w/ 3 levels "4","6","8": 2 2 1 2 3 2 3 1 1 2 ...

# 1 - Map mpg to x and cyl to y
ggplot(mtcars, aes(mpg, cyl)) +
  geom_point()

# 2 - Reverse: Map cyl to x and mpg to y
ggplot(mtcars, aes(cyl, mpg)) +
  geom_point()

# 3 - Map wt to x, mpg to y and cyl to col
ggplot(mtcars, aes(x = wt, y = mpg, col = cyl)) +
  geom_point()

# 4 - Change shape and size of the points in the above plot
## here the shape and size are attributes
## the wt mpg and cyl are mapped to aesthetics, x, y, and color
ggplot(mtcars, aes(wt, mpg, col = cyl)) +
  geom_point(shape = 1, size = 4)

– All about aesthetics, part 2

mtcars$am <- factor(mtcars$am)

# am and cyl are factors, wt is numeric
class(mtcars$am)

## [1] "factor"

class(mtcars$cyl)

## [1] "factor"

class(mtcars$wt)

## [1] "numeric"

# 1 - Map cyl to fill
ggplot(mtcars, aes(x = wt, y = mpg, fill = cyl)) +
  geom_point(shape = 1, size = 4)

This does nothing because shape 1 has no fill value, only color

# 2 - Change shape and alpha of the points in the above plot

ggplot(mtcars, aes(x = wt, y = mpg, fill = cyl)) +
  geom_point(shape = 21, size = 4, alpha= .6)

This changes the fill color of the points but not the border because its shape 21 which has both

# 3 - Map am to col in the above plot
ggplot(mtcars, aes(x = wt, y = mpg, fill = cyl, col = am)) +
  geom_point(shape = 21, size = 4, alpha= .6, stroke = 1.5)

This controls both the fill and border color of shape 21
I adjusted the stroke (or border width) here so I can actually see the border

– All about aesthetics, part 3

# Map cyl to size
ggplot(mtcars, aes(wt, mpg, size = cyl)) + geom_point()

# Map cyl to alpha
ggplot(mtcars, aes(wt, mpg, alpha = cyl)) + geom_point()

# Map cyl to shape 
ggplot(mtcars, aes(wt, mpg, shape = cyl)) + geom_point()

# Map cyl to label
ggplot(mtcars, aes(wt, mpg, label = cyl)) + geom_text()

– All about attributes, part 1

Shapes in R can have a value from 1-25.
- Shapes 1-20 can only accept a color aesthetic
- Shapes 21-25 have both a color and a fill aesthetic.
- See the pch argument in par() for further discussion.
Hex colors are accepted

# 1 - First scatter plot, with col aesthetic:
ggplot(mtcars, aes(wt, mpg, col = cyl)) + 
  geom_point()

# Define a hexadecimal color
my_color <- "#4ABEFF"

# 2 - Plot 1, but set col attributes in geom layer:
ggplot(mtcars, aes(wt, mpg, col = cyl)) + 
  geom_point(col = my_color)

Notice that this removed the legend

# 3 - Plot 2, with fill instead of col aesthetic, plut shape and size attributes in geom layer.
ggplot(mtcars, aes(wt, mpg, fill = cyl)) + 
  geom_point(size = 10, shape = 23, color = my_color, stroke = 1.5)

– All about attributes, part 2

I gotta make the size on these larger or its really hard to see the aesthetics

# Expand to draw points with alpha 0.5
ggplot(mtcars, aes(x = wt, y = mpg, fill = cyl)) +
  geom_point(alpha = 0.5, size = 4)

# Expand to draw points with shape 24 and color yellow
ggplot(mtcars, aes(x = wt, y = mpg, fill = cyl)) +
  geom_point(shape = 24, color = 'yellow', size = 4)

# Expand to draw text with label rownames(mtcars) and color red
ggplot(mtcars, aes(x = wt, y = mpg, fill = cyl)) +
  geom_text(label = rownames(mtcars), color = 'red')

– Going all out

mtcars variables:
- mpg – Miles/(US) gallon
- cyl – Number of cylinders
- disp – Displacement (cu.in.)
- hp – Gross horsepower
- drat – Rear axle ratio
- wt – Weight (lb/1000)
- qsec – 1/4 mile time
- vs – V/S engine.
- am – Transmission (0 = automatic, 1 = manual)
- gear – Number of forward gears
- carb – Number of carburetors

# Map mpg onto x, qsec onto y and factor(cyl) onto col
ggplot(mtcars, aes(mpg, qsec, col = factor(cyl))) + 
  geom_point()

# Add mapping: factor(am) onto shape
ggplot(mtcars, 
  aes(mpg, qsec, 
    col = factor(cyl), 
    shape = factor(am)
    )) + 
  geom_point()

# Add mapping: (hp/wt) onto size
ggplot(mtcars, 
  aes(mpg, qsec, 
    col = factor(cyl), 
    shape = factor(am),
    size = (hp/wt)
    )) + 
  geom_point()

– Aesthetics for categorical and continuous variables

label & shape are restricted to categorical data

Modifying Aesthetics

Position
- identity (most common)
- dodge
- stack
- fill
- jitter
- jitterdodge
Scale names
- 2st part of name is the scale to modify. Every aesthetic has an associated scale function
- 3nd part must match the type of data in the variable (discrete, continuous)
Example scale names
- scale_x_discrete
- scale_y_continuous
- scale_color_…
- scale_fill_…
- scale_shape_…
- scale_linetype_…

– Position

cyl.am <- ggplot(mtcars, aes(x = factor(cyl), fill = factor(am)))

# The base layer, cyl.am, is available for you
# Add geom (position = "stack" by default)
cyl.am + 
  geom_bar()

# Fill - show proportion
cyl.am + 
  geom_bar(position = "fill")

# Dodging - principles of similarity and proximity
cyl.am +
  geom_bar(position = "dodge")

# Clean up the axes with scale_ functions
val = c("#E41A1C", "#377EB8")
lab = c("Manual", "Automatic")
cyl.am +
  geom_bar(position = "dodge") +
  scale_x_discrete(name = "Cylinders") + 
  scale_y_continuous(name = "Number") +
  scale_fill_manual(name = "Transmission", 
                    values = val,
                    labels = lab)

– Setting a dummy aesthetic

## This will give an error because its missing y aesthetic
# ggplot(mtcars, aes(x = mpg)) + geom_point()

# 1 - Create jittered plot of mtcars, mpg onto x, 0 onto y
ggplot(mtcars, aes(x = mpg, y = 0)) +
  geom_jitter()

# 2 - Add function to change y axis limits
ggplot(mtcars, aes(x = mpg, y = 0)) +
  geom_jitter() +
  scale_y_continuous(limits = c(-2,2))

Aesthetics Best Practices

Best aesthetic mappings for continuous variables
Best aesthetic mapping for categorical variables

– Overplotting 1 - Point shape and transparency

# Basic scatter plot: wt on x-axis and mpg on y-axis; map cyl to col
ggplot(mtcars, aes(wt, mpg, col = cyl)) +
  geom_point(size = 4)

# Hollow circles - an improvement
ggplot(mtcars, aes(wt, mpg, col = cyl)) +
  geom_point(size = 4, shape = 1)

# Add transparency - very nice
ggplot(mtcars, aes(wt, mpg, col = cyl)) +
  geom_point(size = 4, alpha = .6)

– Overplotting 2 - alpha with large datasets

# Scatter plot: carat (x), price (y), clarity (color)
ggplot(diamonds, aes(carat, price, col = clarity)) + 
  geom_point()

# Adjust for overplotting
ggplot(diamonds, aes(carat, price, col = clarity)) + 
  geom_point(alpha = 0.5)

# Scatter plot: clarity (x), carat (y), price (color)
ggplot(diamonds, aes(clarity, carat, col = price)) + 
  geom_point(alpha = 0.5)

# Dot plot with jittering
ggplot(diamonds, aes(clarity, carat, col = price)) + 
  geom_point(alpha = 0.5, position = "jitter")

Geometries

Scatter Plots

37 geometries. whaa!
- abline, area, bar, bin2d, blank, boxplot
- contour, crossbar, density, density2d, dotplot
- errorbar, errorbarh, freqpoly, hex, histogram, hline
- jitter, line, linerange, map, path, point, pointrange
- polygon, quantile, raster, rect, ribbon, rug
- segment, smooth, step, text, tile, violin, vline
3 common plots
- scatter plots – points, jitter, abline
- bar plots – histogram, bar, errorbar
- line plots – line
You can also add a nother variable, such as summary statistics in the geom_point
Jitter and alpha are common to deal with overplotting

– Scatter plots and jittering (1)

# Shown in the viewer:
ggplot(mtcars, aes(x = cyl, y = wt)) +
  geom_point()

# Solutions:
# 1 - With geom_jitter()
ggplot(mtcars, aes(x = cyl, y = wt)) +
  geom_jitter()

Thats a little too much jitter
We lose the sense of separate variables
We can adjust the jitter width to fix this

# 2 - Set width in geom_jitter()
ggplot(mtcars, aes(x = cyl, y = wt)) +
  geom_jitter(width = 0.1)

# 3 - Set position = position_jitter() in geom_point() ()
ggplot(mtcars, aes(x = cyl, y = wt)) +
  geom_point(position = position_jitter(0.1))

– Scatter plots and jittering (2)

# Examine the structure of Vocab
library(car)
str(Vocab)

## 'data.frame':    21638 obs. of  4 variables:
##  $ year      : int  2004 2004 2004 2004 2004 2004 2004 2004 2004 2004 ...
##  $ sex       : Factor w/ 2 levels "Female","Male": 1 1 2 1 2 2 1 2 2 1 ...
##  $ education : int  9 14 14 17 14 14 12 10 11 9 ...
##  $ vocabulary: int  3 6 9 8 1 7 6 6 5 1 ...

# Basic scatter plot of vocabulary (y) against education (x). Use geom_point()
ggplot(Vocab, aes(education, vocabulary)) + 
  geom_point()

# Use geom_jitter() instead of geom_point()
ggplot(Vocab, aes(education, vocabulary)) + 
  geom_jitter()

# Using the above plotting command, set alpha to a very low 0.2
ggplot(Vocab, aes(education, vocabulary)) + 
  geom_jitter(alpha = 0.2)

# Using the above plotting command, set the shape to 1
ggplot(Vocab, aes(education, vocabulary)) + 
  geom_jitter(alpha = 0.2, shape = 1)

Bar Plots

– Histograms

# 1 - Make a univariate histogram
ggplot(mtcars, aes(x = mpg)) +
  geom_histogram()

By default the bin width is the range/30

# 2 - Plot 1, plus set binwidth to 1 in the geom layer
ggplot(mtcars, aes(x = mpg)) +
  geom_histogram(binwidth = 1)

We also have access to internal data frame for the plot
We can change the y aes to ..density..
This is calculated internally in the summary stats just like count

# 3 - Plot 2, plus MAP ..density.. to the y aesthetic (i.e. in a second aes() function)
ggplot(mtcars, aes(x = mpg)) +
  geom_histogram(aes(y = ..density..), binwidth = 1)

# 4 - plot 3, plus SET the fill attribute to "#377EB8"
ggplot(mtcars, aes(x = mpg)) +
  geom_histogram(aes(y = ..density..), binwidth = 1, fill = "#377EB8")

– Position

# Draw a bar plot of cyl, filled according to am
ggplot(mtcars, aes(x = cyl, fill = am)) +
  geom_bar()

stack is the default

# Change the position argument to stack
ggplot(mtcars, aes(x = cyl, fill = am)) +
  geom_bar(position = "stack")

# Change the position argument to fill
ggplot(mtcars, aes(x = cyl, fill = am)) +
  geom_bar(position = "fill")

# Change the position argument to dodge
ggplot(mtcars, aes(x = cyl, fill = am)) +
  geom_bar(position = "dodge")

– Overlapping bar plots

# 1 - The last plot form the previous exercise
# ggplot(mtcars, aes(x = cyl, fill = am)) + 
#   geom_bar(position = "dodge")

# 2 - Define posn_d with position_dodge()
posn_d <- position_dodge(width = 0.2)

# 3 - Change the position argument to posn_d
ggplot(mtcars, aes(x = cyl, fill = am)) + 
  geom_bar(position = posn_d)

# 4 - Use posn_d as position and adjust alpha to 0.6
ggplot(mtcars, aes(x = cyl, fill = am)) + 
  geom_bar(position = posn_d, alpha = 0.6)

– Overlapping histograms

# A basic histogram, add coloring defined by cyl 
ggplot(mtcars, aes(mpg, fill = cyl)) +
  geom_histogram(binwidth = 1)

# Change position to identity 
ggplot(mtcars, aes(mpg, fill = cyl)) +
  geom_histogram(binwidth = 1, position = 'identity')

Now the bars are not stacked, but some are hidden behind others

# Change geom to freqpoly (position is identity by default) 
ggplot(mtcars, aes(mpg, col = cyl)) +
  geom_freqpoly(binwidth = 1)

This would look much better with a more full histogram

– Bar plots with color ramp, part 1

Color brewer is a great package for working with colors
Its worth its own chapter probably.

# Example of how to use a brewed color palette
ggplot(mtcars, aes(x = cyl, fill = am)) +
  geom_bar() +
  scale_fill_brewer(palette = "Set1")

# Use str() on Vocab to check out the structure
Vocab$education <- as.factor(Vocab$education)
Vocab$vocabulary <- as.factor(Vocab$vocabulary)
str(Vocab)

## 'data.frame':    21638 obs. of  4 variables:
##  $ year      : int  2004 2004 2004 2004 2004 2004 2004 2004 2004 2004 ...
##  $ sex       : Factor w/ 2 levels "Female","Male": 1 1 2 1 2 2 1 2 2 1 ...
##  $ education : Factor w/ 21 levels "0","1","2","3",..: 10 15 15 18 15 15 13 11 12 10 ...
##  $ vocabulary: Factor w/ 11 levels "0","1","2","3",..: 4 7 10 9 2 8 7 7 6 2 ...

# Plot education on x and vocabulary on fill
# Use the default brewed color palette
ggplot(Vocab, aes(x = education, fill = vocabulary)) +
  geom_bar(position = 'fill') + 
  scale_fill_brewer()

There are only 9 colors in the “Blues” palette, but we have 11 categories under vocabulary
- So we get an error. And a weird looking chart. groups 9 and 10 are blank
- We need to create our own palette with the same number of colors as groups

– Bar plots with color ramp, part 2

A quick example of how the colorRampPalette works
- It returns a function that can be used to make a new palette
- You can just use two colors and it will scale between them
- Or you can use many colors or an existing palette

new_col <- colorRampPalette(c("#FFFFFF", "#0000FF"))
new_col(4) # the newly extrapolated colours

## [1] "#FFFFFF" "#AAAAFF" "#5555FF" "#0000FF"

munsell::plot_hex(new_col(4)) # Quick and dirty plot

library(RColorBrewer)

# Final plot of last exercise
ggplot(Vocab, aes(x = education, fill = vocabulary)) +
  geom_bar(position = "fill") +
  scale_fill_brewer()

# Definition of a set of blue colors
blues <- brewer.pal(9, "Blues") # from the RColorBrewer package
blues

## [1] "#F7FBFF" "#DEEBF7" "#C6DBEF" "#9ECAE1" "#6BAED6" "#4292C6" "#2171B5"
## [8] "#08519C" "#08306B"

# 1 - Make a color range using colorRampPalette() and the set of blues
blue_range <- colorRampPalette(blues)

# This is our new pallete. We can create it with as many colors as we want. 
munsell::plot_hex(blue_range(11))

# 2 - Use blue_range to adjust the color of the bars, use scale_fill_manual()
ggplot(Vocab, aes(x = education, fill = vocabulary)) +
  geom_bar(position = "fill") +
  scale_fill_manual(values = blue_range(11))

- Nice. Thats much better.

– Overlapping histograms (2)

# 1 - Basic histogram plot command
ggplot(mtcars, aes(mpg)) + 
  geom_histogram(binwidth = 1)

# 2 - Plot 1, Expand aesthetics: am onto fill
ggplot(mtcars, aes(mpg, fill = am)) + 
  geom_histogram(binwidth = 1)

# 3 - Plot 2, change position = "dodge"
ggplot(mtcars, aes(mpg, fill = am)) + 
  geom_histogram(binwidth = 1, position = "dodge")

# 4 - Plot 3, change position = "fill"
## In this case, none of these positions really work well, because it's difficult to compare the distributions directly.
ggplot(mtcars, aes(mpg, fill = am)) + 
  geom_histogram(binwidth = 1, position = "fill")

# 5 - Plot 4, plus change position = "identity" and alpha = 0.4
ggplot(mtcars, aes(mpg, fill = am)) + 
  geom_histogram(binwidth = 1, 
    position = "identity",
    alpha = 0.4)

# 6 - Plot 5, plus change mapping: cyl onto fill
ggplot(mtcars, aes(mpg, fill = cyl)) + 
  geom_histogram(binwidth = 1, 
    position = "identity",
    alpha = 0.4)

Line Plots - Time Series

– Line plots

# Print out head of economics
head(economics)

## # A tibble: 6 x 6
##         date   pce    pop psavert uempmed unemploy
##       <date> <dbl>  <int>   <dbl>   <dbl>    <int>
## 1 1967-07-01 507.4 198712    12.5     4.5     2944
## 2 1967-08-01 510.5 198911    12.5     4.7     2945
## 3 1967-09-01 516.3 199113    11.7     4.6     2958
## 4 1967-10-01 512.9 199311    12.5     4.9     3143
## 5 1967-11-01 518.1 199498    12.5     4.7     3066
## 6 1967-12-01 525.8 199657    12.1     4.8     3018

# Plot unemploy as a function of date using a line plot
ggplot(economics, aes(x = date, y = unemploy)) +
  geom_line()

# Adjust plot to represent the fraction of total population that is unemployed
ggplot(economics, aes(x = date, y = unemploy/pop)) +
  geom_line()

– Periods of recession

# Basic line plot
# ggplot(economics, aes(x = date, y = unemploy/pop)) +
#   geom_line()

# Expand the following command with geom_rect() to draw the recess periods
ggplot(economics, aes(x = date, y = unemploy/pop)) +
  geom_rect(data = recess,
         aes(xmin = begin, 
             xmax = end, 
             ymin = -Inf, 
             ymax = Inf),
            inherit.aes = FALSE,
            fill = "red", 
            alpha = 0.2
            ) + 
  geom_line()

– Multiple time series, part 1

# Check the structure as a starting point
str(fish.species)

## 'data.frame':    61 obs. of  8 variables:
##  $ Year    : int  1950 1951 1952 1953 1954 1955 1956 1957 1958 1959 ...
##  $ Pink    : int  100600 259000 132600 235900 123400 244400 203400 270119 200798 200085 ...
##  $ Chum    : int  139300 155900 113800 99800 148700 143700 158480 125377 132407 113114 ...
##  $ Sockeye : int  64100 51200 58200 66100 83800 72000 84800 69676 100520 62472 ...
##  $ Coho    : int  30500 40900 33600 32400 38300 45100 40000 39900 39200 32865 ...
##  $ Rainbow : int  0 100 100 100 100 100 100 100 100 100 ...
##  $ Chinook : int  23200 25500 24900 25300 24500 27700 25300 21200 20900 20335 ...
##  $ Atlantic: int  10800 9701 9800 8800 9600 7800 8100 9000 8801 8700 ...

# Use gather to go from fish.species to fish.tidy
fish.tidy <- gather(fish.species, Species, Capture, -Year)

str(fish.tidy)

## 'data.frame':    427 obs. of  3 variables:
##  $ Year   : int  1950 1951 1952 1953 1954 1955 1956 1957 1958 1959 ...
##  $ Species: chr  "Pink" "Pink" "Pink" "Pink" ...
##  $ Capture: int  100600 259000 132600 235900 123400 244400 203400 270119 200798 200085 ...

– Multiple time series, part 2

# Recreate the plot shown on the right
ggplot(fish.tidy, aes(x = Year, y = Capture, col = Species)) +
  geom_line()

qplot and wrap-up

qplot

qplot is sort of the base R eqivalent in terms of syntax
- you can make charts quick and easy. It will guess the geom for you
But its better just to know the ggplot layers and be explicit and build your plots.
- This is intuative and not that much more typing.
- Its still good to know about qplot because you will see it

– Using qplot

# The old way (shown)
plot(mpg ~ wt, data = mtcars) # formula notation

with(mtcars, plot(wt, mpg)) # x, y notation

# Using ggplot:
ggplot(mtcars, aes(wt, mpg)) +
  geom_point()

# Using qplot:
qplot(wt, mpg, data = mtcars)

– Using aesthetics

# Categorical variable mapped onto size:
# cyl
qplot(wt, mpg, data = mtcars, size = factor(cyl))

# gear
qplot(wt, mpg, data = mtcars, size = factor(gear))

# Continuous variable mapped onto col:
# hp
qplot(wt, mpg, data = mtcars, col = hp)

# qsec
qplot(wt, mpg, data = mtcars, col = qsec)

– Choosing geoms, part 1

# qplot() with x only
qplot(x = factor(cyl), data = mtcars)

# qplot() with x and y
qplot(x = factor(cyl), y = factor(vs), data = mtcars)

# qplot() with geom set to jitter manually
qplot(x = factor(cyl), y = factor(vs), data = mtcars, geom = 'jitter')

– Choosing geoms, part 2 - dotplot

# cyl and am are factors, wt is numeric
class(mtcars$cyl)

## [1] "factor"

class(mtcars$am)

## [1] "factor"

class(mtcars$wt)

## [1] "numeric"

# "Basic" dot plot, with geom_point():
ggplot(mtcars, aes(cyl, wt, col = am)) +
  geom_point(position = position_jitter(0.2, 0))

# 1 - "True" dot plot, with geom_dotplot():
ggplot(mtcars, aes(cyl, wt, fill = am)) +
  geom_dotplot(binaxis = "y", stackdir = "center")

# 2 - qplot with geom "dotplot", binaxis = "y" and stackdir = "center"
qplot(
  cyl, wt, 
  data = mtcars, 
  fill = am, 
  geom = "dotplot", 
  binaxis = "y", 
  stackdir = "center"
)

Wrap-up

– Chicken weight

# ChickWeight is available in your workspace
# 1 - Check out the head of ChickWeight
head(ChickWeight)

## Grouped Data: weight ~ Time | Chick
##   weight Time Chick Diet
## 1     42    0     1    1
## 2     51    2     1    1
## 3     59    4     1    1
## 4     64    6     1    1
## 5     76    8     1    1
## 6     93   10     1    1

# 2 - Basic line plot
ggplot(ChickWeight, aes(x = Time, y = weight)) + 
  geom_line(aes(group = Chick))

# 3 - Take plot 2, map Diet onto col.
ggplot(ChickWeight, 
    aes(x = Time, y = weight, col = Diet)) + 
  geom_line(
    aes(group = Chick))

# 4 - Take plot 3, add geom_smooth()
ggplot(ChickWeight, 
    aes(x = Time, y = weight, col = Diet)) + 
  geom_line(
    aes(group = Chick), alpha = 0.3) + 
  geom_smooth(lwd = 2, se = F)

– Titanic

# titanic is avaliable in your workspace
# 1 - Check the structure of titanic
str(titanic)

## 'data.frame':    714 obs. of  4 variables:
##  $ Survived: int  0 1 1 1 0 0 0 1 1 1 ...
##  $ Pclass  : int  3 1 3 1 3 1 3 3 2 3 ...
##  $ Sex     : Factor w/ 2 levels "female","male": 2 1 1 1 2 2 2 1 1 1 ...
##  $ Age     : num  22 38 26 35 35 54 2 27 14 4 ...

# 2 - Use ggplot() for the first instruction
ggplot(titanic, 
    aes(x = Pclass, fill = Sex)) + 
  geom_bar(
    position = "dodge")

# 3 - Plot 2, add facet_grid() layer
ggplot(titanic, 
    aes(x = Pclass, fill = Sex)) + 
  geom_bar(
    position = "dodge") +
  facet_grid(. ~ Survived)

# 4 - Define an object for position jitterdodge, to use below
posn.jd <- position_jitterdodge(0.5, 0, 0.6)

# 5 - Plot 3, but use the position object from instruction 4
ggplot(titanic, 
    aes(x = Pclass, y = Age, col = Sex)) + 
  geom_point(
    size = 3, alpha = 0.5, position = posn.jd) +
  facet_grid(. ~ Survived)

Data Visualization with ggplot2 (Part 1)

William Surles

2017-07-26

My Introduction

Whats Covered

Aditional Resources

Introduction

Introduction

– Explore and Explain

– Exploring ggplot2, part 1

– Exploring ggplot2, part 2

Grammar of Graphics

– Exporing ggplot2, part 3

– Understanding variables

ggplot2

– Exploring ggplot2, part 4

– Exploring ggplot2, part 5

– Understanding the grammar, part 1

– Understanding the grammar, part 2

Data

Objects and Layers

– base package and ggplot2, part 1 - plot

– base package and ggplot2, part 2 - lm

– base package and ggplot2, part 3

– ggplot2 compared to base package

Tidy Data

– Variables to visuals, tidy dataset

– Variables to visuals, tidy chart

– Variables to visuals, wide dataset

– Variables to visuals, wide chart

Aesthetics

Visible Aesthetics

– All about aesthetics, part 1

– All about aesthetics, part 2

– All about aesthetics, part 3

– All about attributes, part 1

– All about attributes, part 2

– Going all out

– Aesthetics for categorical and continuous variables

Modifying Aesthetics

– Position

– Setting a dummy aesthetic

Aesthetics Best Practices

– Overplotting 1 - Point shape and transparency

– Overplotting 2 - alpha with large datasets

Geometries

Scatter Plots

– Scatter plots and jittering (1)

– Scatter plots and jittering (2)

Bar Plots

– Histograms

– Position

– Overlapping bar plots

– Overlapping histograms

– Bar plots with color ramp, part 1

– Bar plots with color ramp, part 2

– Overlapping histograms (2)

Line Plots - Time Series

– Line plots

– Periods of recession

– Multiple time series, part 1

– Multiple time series, part 2

qplot and wrap-up

qplot

– Using qplot

– Using aesthetics

– Choosing geoms, part 1

– Choosing geoms, part 2 - dotplot

Wrap-up

– Chicken weight

– Titanic